by Mark Dempsey, CFSA Farm Services Manager | Monday, November 14, 2022 —
Field of green leaves and red crimson clover flowers

As the season comes to a close, you may not be thinking much about nitrogen (N) management on your farm.

However, since plants need nitrogen more than other nutrients, and it is the most difficult nutrient to manage, this is an invitation to do just that for next year. Take some time—now or over the winter—to consider how the following three steps may be a pathway to better N management on your farm—potentially saving you money, improving crop quality and yields, and reducing pollution downstream and in the air.

“There’s a lot of new research that can inform how to choose and when to apply organic fertilizers, and there are a few nitrogen management principles to be aware of to minimize losses and ensure the best use of nitrogen on your farm.”

While these steps are laid out in detail below, the summary is that there’s a lot of new research that can inform how to choose and when to apply organic fertilizers, and there are a few N management principles to be aware of to minimize losses and ensure the best use of N on your farm.


1) Leverage soil biology for better nitrogen management

Use legume cover crops in your rotation to take advantage of N fixation. Select cover crop species that fit your season and N needs, and terminate them around flowering to take the best advantage of fixed N.

Minimize soil disturbance and maximize live roots in the ground to favor arbuscular mycorrhizal fungi, which help with N uptake.

Remember that most N in organic fertilizers must be transformed to be plant-available.


2) Carefully choose nitrogen fertilizers

Select these based on the N they contain (both plant-available and organic forms) and the timeframe in which organic N will be converted to plant-available N.

Some organic fertilizers release N rather quickly, some release N rather slowly, and many are in between. Take phosphorus into account when using manure and manure-based compost, as excess phosphorus can lead to downstream pollution.


3) Minimize nitrogen losses

Consider other management factors to minimize N losses, which come at a cost to your bottom line, as well as to human and environmental health.

To reduce nitrate leaching, avoid nitrate-based fertilizers, and for all other fertilizer materials—which are transformed to ammonium—incorporate them into the soil or under mulches. If you’re growing in sandy soil or degraded clay, then focus on building soil organic matter to bind ammonium.

To reduce gaseous losses, incorporate manure and fertilizer into soil or under mulches (reducing ammonia volatilization) and avoid waterlogged conditions (reducing denitrification).


If you’d like to learn more about each of these steps, read on. We’ve done our best to gather the best information on each of these steps and hope you find it useful.


Nitrogen (N) is the most complex nutrient to manage, as soil microbes are forever changing N in soil from one form to another. Much of the N in soil is taken up by plants as nitrate (NO3) and ammonium (NH4+), tied up by microbes to break down carbon-rich organic matter or is temporarily bound to clay and soil organic matter.

Unfortunately, many of the N forms in soil are lost either by leaching (NO3) or as gases (NH3, N2, NO2, NO, and N2O); these loss processes occur naturally and are difficult to control. Nitrogen contained in organic matter (e.g., terminated cover crops, compost, and many organic fertilizers) is by and large not available to plants until it is decomposed, first to NH4+, some of which is then transformed to NO3.

As promised above, let’s dive into how N behaves in soil and beyond and how to get the most N to your crops while minimizing losses and pollution.


 1. Leverage Soil Biology: Nitrogen Fixation, Mycorrhizal Fungi & Decomposition

Did you know that before the invention of industrial N fixation over 100 years ago, biological N fixation was the bottleneck for N available to virtually all life on the planet? Biological N fixation is carried out by bacteria that convert atmospheric N (N2) to NH3, which converts to bioavailable NH4+. In agriculture, this is mostly the work of Rhizobia and related bacteria in the nodules of legumes. While biological N fixation happens in other bacteria partnered with other crops (e.g., sugarcane, sweet potato, finger millet, carrot, and radish), legumes help to fix far more N than other crop species.

Close up of white clover in a field

White clover blossoms.


Legumes grown as cover crops are of particular interest because they aren’t harvested; therefore, more of the fixed N stays in the field and is available to subsequent crops. Legume cover crops should be a part of every N management plan. They’re easy to incorporate into a rotation. They also have many co-benefits, such as increased biological activity and diversity in your soil and other potential improvements like better soil structure and water infiltration and retention (compared to simply adding an N fertilizer).

Thoughts on nitrogen availability after a legume cover crop:

  • The amount of N fixed by legume cover crops depends on the cover crop species (Table 1) and how long they’re left in the ground before termination. As a general rule, allowing legume cover crops to reach flowering maximizes fixed N availability. If you terminate earlier, you lose out on potential N fixation. If you terminate later, then short-term N availability decreases because seed development converts plant-available N into proteins, which require decomposition to be plant-available once again.
  • Second, the availability of fixed N depends on how quickly the cover crop decomposes, which in turn depends on whether the cover crop is on the soil surface (slowest to decompose), incorporated into the soil (fastest), or covered by a mulch (intermediate). Additionally, the ratio of carbon to nitrogen (C:N) in cover crops is the next most important factor determining N release. More fibrous cover crops (higher C:N) release N slower than less fibrous ones (lower C:N). Sunn hemp (Crotalaria juncea) and chickpea (Cicer arietinum) are good examples of fibrous legumes, whereas cowpea (Vigna unguiculata) and winter pea (Pisum sativum) are less fibrous.
Table One
Table 1. Typical amount of nitrogen (N) fixed and dry biomass of various legume cover crop species, and their corresponding inoculation species. Fixed N and biomass values are from Managing Cover Crops Profitably unless otherwise noted at the bottom of this article.


Don’t forget to inoculate legumes with the right Rhizobia species (Table 1), particularly if you haven’t grown that particular cover crop in that location for more than three years.

A final note on legume cover crops for N: If you use manure for soil fertility, remember that it is relatively high in phosphorus (P) compared to crop N needs. Therefore manure application can easily lead to excess soil P and downstream P pollution. The best way to handle this problem is to apply manure at a lower rate – determined by your crop’s P demand instead of N demand – and rely on a legume cover crop to make up the rest of the N needed by your crop. If more N is needed, supplement with more concentrated N sources to avoid excess P and potential pollution.

Hairy vetch and wheat cover crops ready for crimping. The wheat has flowered, and the vetch is forming pods, which means they can be successfully terminated with a crimper. Photo credit: John Wallace


Arbuscular mycorrhizal (AM) fungi live in symbiosis with the majority of plants, where they improve nutrient and water access to plants in return for sugar and lipids. While AM fungi have long been known to improve crop access to P in soil, recent research has shown that they also help crops to acquire N (see Bücking and Kafle, 2015). AM fungi have the hardware, so to speak, needed to uptake and transport N to plants, including organic N that plants uptake only in small quantities1 (e.g., amino acids). Combined with the fact that they also dramatically increase the reach of plant roots by exploring further into soil, AM fungi can improve access to N, water, and other nutrients for crops. Thankfully, the vast majority of crops support the symbiosis with AM fungi—the important exception being brassicas (cole crops). Mycorrhizal relationships are favored by reducing soil disturbance and maintaining live roots in the ground for as much of the year as possible.

Finally, a note on decomposition: remember that organic N forms, by in large, must be decomposed (mineralized) in order to become plant available1, including those contained in cover crops and the fertilizers detailed in the next section. This is the work of the countless decomposers in soil, whose abundance and diversity have a positive influence on decomposition; these are increased by implementing soil health principles such as minimizing soil disturbance and maximizing live roots and soil coverage. To read more about implementing soil health principles in the Southeastern U.S., check out our write-up: Soil Health for Crop Producers in the Southeast: 5 Management Priorities and OFRF’s fantastic resource, Building Health Living Soils for Successful Organic Farming in the Southern Region

Crimson clover is a popular annual legume cover crop that can be used in both no-till and tillage-based systems. Credit: John Wallace.


 2. Fertilizer Selection: Synchronizing Nitrogen Supply with Demand

There are many fertilizer and manure options to provide crops with N. These supply N mostly as urea (manure slurries from mammals2), uric acid (manure/litter from birds2), and various organic N forms from animal processing byproducts (e.g., feather meal and blood meal) or from plant material (e.g., alfalfa meal). All the N forms in those fertilizers and manures are microbially converted first to ammonium (NH4+), a plant-available form, and then to nitrate (NO3; also plant-available), as well as gaseous N forms. There is only one non-synthetic NO3-based fertilizer that is commonly used, sodium nitrate or Chilean nitrate, although many synthetic NO3-based fertilizers are common in conventional production. Nitrate does not need to be microbially transformed to be plant-available. It is highly soluble in water and immediately available to plants once in the soil solution but is easily leached below the root zone.

Remember that N is primarily available to plants as NH4+ and NO3; therefore, all organic N forms (i.e., compounds containing both carbon and N), in general, must be decomposed or mineralized to plant-available forms1. Organic N sources are mineralized to NH4+ first, then microbially transformed to NO3, among other transformations. See the “Minimize N Losses” section, below, about the contrasting behavior of NH4+ vs. NO3- in soil and its importance for crop use. 

The fact that organic N forms must be mineralized to be plant-available is important for two reasons:

  • Total Nitrogen: The percent N on a bag of fertilizer or manure (the first number of the 3-number nutrient analysis that is standard on all fertilizers) represents total N, not plant-available N, and much of the N in manure and organic fertilizers must be mineralized to be plant-available.
  • Mineralization Rates: These common fertility sources have vastly different N mineralization rates, and insight into these rates is the first critical step in matching N supply from fertilizers to your crop’s N demand. The second step is understanding how much—and when—your crop needs N.

Studies on mineralization rates of organic fertilizers have shown striking differences in how quickly the organic N they contain is mineralized.

An excellent study published by Cassity-Duffy et al. (2020) compared mineralization rates among several organic fertilizers, poultry manures, and composts (Table 2). The study was done in only one soil type (Cecil sandy loam), and will not apply to everyone’s conditions, but it informs how mineralization rates among different fertility materials compare to each other.

They found that:

  • Feather meal and blood meal N are mineralized very quickly, releasing >60% of the organic N they contain after 21 days of incorporating into soil, and approx. 80% – 90% after 99 days (Figure 1a; Table 2). Those are your go-to fertilizers for rapid N release.
  • Poultry litter N mineralization ranged from 10% – 30% after 21 days, and 25% – 55% after 99 days (Figure 1b; Table 2). Poultry litter is an excellent choice for medium-term N release.
  • Bone meal released approx. 15% of the N it contains after 21 days, and 25% after 99 days. Bone meal is most often used to meet P needs, not necessarily N needs, although N should be accounted for in a nutrient budget.
  • The compost tested in this study mineralized very slowly, although among the 11 different composts tested, mineralization was variable: some composts released nearly 5% of the organic N they contain over the 99-day incubation, while others tied it up (immobilized), making less N available (Figure 1c; Table 2). Compost is best used as a long-term soil builder and not a near-term N source.
Table 2
Table 2. Nutrient content (percent N, P2O5 & K2O) of various manures, composts, and non-synthetic fertilizers. The ratio of carbon to nitrogen (C:N) is shown because it relates to the rate at which organic N is decomposed (mineralized). Results of a 99-day incubation study are shown for net mineralization of organic N and total plant-available N from select materials. Data sources are provided at the bottom of this article.
Figure 1
Figure 1. Net nitrogen mineralization (as a % of organic N applied) for organic fertilizers (a) poultry litter (b) and compost (c) incubated in a Cecil sandy loam soil for 99 days. Among organic fertilizers, “Pellet 5” contains pelleted poultry litter and/or other animal and bone meal, and “Mix 3” contains a combination of animal, bone, and blood meal. Note different scales between graphs. Adapted from Cassity-Duffey et al., (2020). Note that only 4 of the 15 poultry litters and 3 of the 11 composts are shown; see Table 2 for averages across all poultry litters and composts tested.


Remember that manures and manure-based composts tend to be high in P relative to crop demand. These are a concern for downstream P pollution and should be applied based on the crop’s P needs and a nutrient analysis of the manure or compost to avoid excess P in soil. Additional N needs should be made up using legume cover crops and/or other N sources.

Additionally, the release of plant-available N from the decomposition of cover crops with high C:N ratios, such as small grains, will take longer than cover crops with lower C:N ratios, such as legumes and brassicas. It is not uncommon for a small grain cover crop (e.g., winter rye) to reduce the amount of N available to the subsequent cash crop. This can be accounted for by adding more N fertilizer or by using a legume or legume and small grain cover crop mixture.


3. Minimize Nitrogen Losses

Making the best use of N fertilizers on your farm—minimizing N losses—primarily comes down to the simple distinction between the two forms of plant-available N: nitrate (NO3) and ammonium (NH4+), which have opposite ionic charges, and as a result, behave differently in soil. Specifically, it is the positive charge of NH4+ that temporarily binds to negatively charged clay and organic matter in soil, preventing it from leaching and keeping it near plant roots for uptake. The negative charge of NO3, on the other hand, does not bind with clay and organic matter, and thus NO3 is easily leached from soil3.

Again, the urea and uric acid in animal manures—as well as organic N forms in animal processing byproducts (e.g., feather meal and blood meal) and plant material (e.g., alfalfa meal)—are transformed first to NH4+, and then to NO3. This is good because the NH4+ that plants do not immediately take up has the chance to temporarily bind to clay and organic matter in the root zone. In contrast, NO3-based fertilizers such as sodium nitrate are a concern because NO3 is easily leached when NO3 supply exceeds demand by plants. Anyone using synthetic NO3 fertilizers such as ammonium nitrate, calcium nitrate, or potassium nitrate should heed the same warning. One caveat to all this: no N form in soil is stable, and NH4+ will eventually (often quickly) convert to NO3 via nitrification, where it can be lost to leaching. However, the initial binding of NH4+ to clay and organic matter keeps it in the root zone longer and increases the chances of plant uptake, compared to NO3 applied directly.

Incorporating fertilizers into soil with tillage helps reduce nitrogen losses, but if you don’t use tillage, applying them in standing cover crops which are then mowed or crimped is the next best way to keep them in contact with soil to minimize nitrogen losses. Photo credits: John Wallace.


It is noteworthy that in sandy soils, where both clay and organic matter are low, NO3 leaching can be problematic regardless of fertilizer type because there are few binding sites for NH4+ before it transforms to NO3. Additionally, there are many locations in the Southeastern U.S. where the topsoil has long been eroded, and the remaining subsoil (highly weathered kaolinite clay) has a limited ability to hold onto NH4+ (i.e., low cation exchange capacity, CEC, often <5 meq/100g). Thus, producers growing in sandy soil or highly weathered clay (i.e., soils with low CEC) should focus on building soil organic matter to improve CEC to mitigate NO3 leaching and make better use of applied N. Two ways to do this are through using compost and cover crops.

There are also two gaseous N loss pathways to be aware of and try to manage.

  • The first is ammonia volatilization, which is the loss of ammonia (NH3) gas after the N compounds in manures (urea and uric acid) and organic fertilizers are transformed to NH4+ and then to gaseous NH3. Air pollution from NH3 volatilization produced from agriculture poses environmental and human health risks, and NHlosses also come at an economic cost. Ammonia volatilization can be mitigated by incorporating manures and fertilizers into soil or under mulches (cover crop, compost, or otherwise), followed by rainfall or irrigation. These practices help to reduce NH3 volatilization by putting NH4+ in contact with clay and organic matter in soil, where they’re temporarily bound up and kept near plant roots for uptake. Thus, manures and organic N fertilizers should never be applied to the soil surface without further action; if left on the soil surface, a large proportion of the applied N (often 25%-40%) will be lost as NH3 gas. Additionally, soil pH values above 7 increase NH3 volatilization, and pH should be managed between 5.5 and 7 to minimize volatilization and optimize nutrient management.
  • The second gaseous loss pathway is denitrification, which is the microbial conversion of NO3 to N2 (i.e., atmospheric N), with three intermediate gases also lost to the atmosphere: NO2, NO, and N2O. It is noteworthy that these intermediate gaseous forms, NO2, NO, and N2O, are pollutants: NO and N2O contribute to acid rain (as nitric acid), NO2 can contribute to harmful smog, N2O is a potent greenhouse gas in the upper atmosphere (300x CO2equivalent), and all three in the stratosphere can contribute to the depletion of the ozone layer. Denitrification occurs under waterlogged conditions and can be mitigated by avoiding these conditions—not always possible in heavy soils—but can be somewhat managed by avoiding low-lying areas, using raised beds, alleviating compaction, and possibly by using tillage to hasten soil drying (although tillage should be avoided when soil is too wet).

Conclusions: How to Apply This Info to the Farm

It is our hope that by working with these three concepts—relying on soil biology, careful fertilizer selection and management, and minimizing N losses—you can improve N management on the farm, ultimately leading to better crops, more profits, and less downstream pollution.

If you have any questions, please follow up with Mark Dempsey: [email protected]


1 Much research has demonstrated that crops are able to take up some organic N forms, however quantifying that amount has proven difficult, and we don’t know the significance of direct organic N uptake by crops. We may well learn in the coming years that crops are well-equipped to use organic N sources, but given our current knowledge and uncertainty, this article assumes that direct organic N use by crops is low.
2 The urea contained in manure slurries from mammalian livestock comes primarily from urine and less so from manure. In contrast, avian livestock have only one type of waste excreta, which is referred to simply as manure and is rich in uric acid. Mammals and birds process N differently, with mammals excreting waste N as urea and birds as uric acid. Because of this difference, manure from avian livestock tends to have a higher N proportion.
3 The old, weathered clays in the Southeast are dominated by kaolinite clay and iron and aluminum oxides, particularly deep in subsoil. This gives these soils both positive and negative binding sites—referred to as variable surface charge—and, therefore, the ability to bind negative ions such as NO3 in subsoil, reducing leaching into groundwater. That NO3 is thought to be out of reach of most crop roots, but it is unclear if long-season or perennial crops can access it.
Table 1
A N fixation values are 25th to 75th quartile data from Gaskin et al. (2016).
B Personal observations. Dempsey, M. & Battle, P.
Table 2:
a N content and mineralization values from Cassity-Duffey et al., (2020).
b N content and mineralization values are the mean of 15 poultry manure samples and 11 compost samples analyzed by Cassity-Duffey et al., (2020). Standard error of means are shown after ± symbol. Note that net mineralization and plant-available N for compost samples represents maximum potential values and likely over-estimates both metrics, as N was immobilized in 5 of the 11 compost samples; zeros were used for these immobilized samples.
c N, P2O5, and K2O values taken from Penn State’s Organic Crop Production Guide Table 5.11 (Beegle and Stehouwer, 2015), unless N values specified from Cassity-Duffey et al., (2020). Manure nutrient content values are highly variable; a narrow range of means is reported from different sources for simplicity.
d N, P2O5, and K2O values taken from common products such as those manufactured by NatureSafe or sold through well-known vendors such as Seven Springs Farm Supply (Check, VA), and products listed on Organic Materials Review Institute’s (ORMI) website.
e from Chastain et al. (1999) Swine Manure Production and Nutrient Content.
f Midwest Planning Service Livestock Waste Facilities Handbook, 1993.
g Limited data. The majority of N in cattle and swine manure is urea-N; it is not organic and not mineral (NH4+ or NO3), however the addition of bedding material converts urea-N to organic N while also increasing C:N; data is limited and variable.
h Sodium nitrate contains no organic N; 4% of the NO3 was immobilized by soil microbes.
Literature Cited
Beegle, D., Stehouwer, R. 2015. Soil Fertility. In: Penn State Organic Production Guide; Publications Distribution Center, The Pennsylvania State University.
Bücking, H. and Kafle, A. 2015. Role of Arbuscular Mycorrhizal Fungi in the Nitrogen Uptake of Plants: Current Knowledge and Research Gaps. Agronomy Journal 5, 587-612.
Cassity-Duffey, K., Cabrera, M., Gaskin, J., Franklin, D., Kissel, D., Saha, U. 2020. Nitrogen mineralization from organic materials and fertilizers: Predicting N release. Soil Science Society of America Journal 84, 522-523.
Chastain, J., Camberato, J., Albrecht, J., Adams, J. 1999. Swine manure production and nutrient content. In: South Carolina Confined Animal Manure Managers Certification Program. Clemson University, SC, USA (Chapter 3).
Gaskin, J., Cabrera, M., Kissel, D. 2016. The Cover Crop Nitrogen Availability Calculator. University of Georgia Extension Bulletin 1466.
Managing Cover Crop Profitably, 3rd ed. 2012. Sustainable Agriculture Research & Education (SARE)
Midwest Planning Service Livestock Waste Facilities Handbook, 1993.